Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway  

作　　者：Hong-Lei Li Lin Wu Zhaoming Dong Yusong Jiang Sanjie Jiang Haitao Xing Qiang Li Guocheng Liu Shuming Tian Zhangyan Wu Bin Wu Zhexin Li Ping Zhao Yan Zhang Jianmin Tang Jiabao Xu Ke Huang Xia Liu Wenlin Zhang Qinhong Liao Yun Ren Xinzheng Huang Qingzhi Li Chengyong Li Yi Wang Baskaran Xavier-Ravi Honghai Li Yang Liu Tao Wan Qinhu Liu Yong Zou Jianbo Jian Qingyou Xia Yiqing Liu 

机构地区：[1]College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China [2]Engineering Research Center for Special Plant Seedlings of Chongqing,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China [3]State Key Laboratory of Silkworm Genome Biology,Biological Science Research Center,Southwest University,Beibei,Chongqing,China [4]BGI Genomics,BGI-Shenzhen,Shenzhen,Guangdong,China [5]College of Biology and Food Engineering,Chongqign Three Gorges University,Wanzhou,Chongqing,China [6]Department of Entomology and MOAKey Lab of Pest Monitoring and Green Management,College of Plant Protection,China Agricultural University,Haidian,Beijing,China [7]Jinan Second Agricultural Science Research Institute,Jinan,Shandong,China [8]Savari Research Foundation,Mela Ilandai Kulam,Tamil Nadu,India [9]Institute of Advanced Interdisciplinary Studies,Chongqing University,Chongqing,China [10]Fairy Lake Botanical Garden and Chinese Academy of Sciences,Shenzhen,Guangdong,China [11]Ningyang Science and Technology Bureau,Taian,Shandong,China [12]College of Horticulture and Gardening,Yangtze University,Jingzhou,Hubei,China

出　　处：《Horticulture Research》2021年第1期2546-2558,共13页园艺研究（英文）

基　　金：This work was supported by funding from the Ginger Genome Project of Chongqing University of Arts and Sciences(2018);the Natural Science Foundation of Chongqing(cstc2019jcyj-msxmX0300,cstc2019jcyj-msxmX0697,CQYC201903201,cstc2019jscx-dxwtBX0028);the Foundation for High-level Talents of Chongqing University of Arts and Science(2017RTZ21,P2018TZ05);the Scientific and Technological Research Program of Chongqing Municipal Education Commission(KJZD-K202001304,KJQN201801339,KJQN201801330,KJQN201801335);the Foundation of Hubei Rural Science and Technology(2020BBA037);the State Key Research and Development Program of Hubei(2020BBA037);the Foundation of Laiwu Experimental Station of the National Characteristic Vegetable Industry System.

摘　　要：Ginger(Zingiber officinale),the type species of Zingiberaceae,is one of the most widespread medicinal plants and spices.Here,we report a high-quality,chromosome-scale reference genome of ginger‘Zhugen’,a traditionally cultivated ginger in Southwest China used as a fresh vegetable,assembled from PacBio long reads,Illumina short reads,and high-throughput chromosome conformation capture(Hi-C)reads.The ginger genome was phased into two haplotypes,haplotype 1(1.53 Gb with a contig N50 of 4.68 M)and haplotype 0(1.51 Gb with a contig N50 of 5.28 M).Homologous ginger chromosomes maintained excellent gene pair collinearity.In 17,226 pairs of allelic genes,11.9%exhibited differential expression between alleles.Based on the results of ginger genome sequencing,transcriptome analysis,and metabolomic analysis,we proposed a backbone biosynthetic pathway of gingerol analogs,which consists of 12 enzymatic gene families,PAL,C4H,4CL,CST,C3’H,C3OMT,CCOMT,CSE,PKS,AOR,DHN,and DHT.These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs.Overall,this study serves as an excellent resource for further research on ginger biology and breeding,lays a foundation for a better understanding of ginger evolution,and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

关 键 词：backbone maintained analogs 

分 类 号：Q943.2[生物学—植物学]